GROMACS version: 2020
GROMACS modification: No
I have run a protein-DNA simulation with the protein placed about 8 angstroms away from the DNA molecule. I see that at the end of the trajectory, they have come closer. However the DNA seems to be extremely distorted, even the base pairing has been disrupted in between. I have attached a picture of the last frame. Does this usually happen in simulations? What could be the mistakes? How do I calculate or test if there are any interactions between the DNA and the protein.
Kindly let me know.
What force field are you using?
Also, if you want to check whether or not distortion is induced by the protein, you should be doing a control simulation of the DNA alone to understand its dynamics.
charmm36m,
I used the input generator on charmmgui for this. Will do a control simulation on the DNA as well. It would be really helpful if you could provide me a basic workflow on how to setup DNA-protein simulations as well as I am new to this and just tested this out for fun.
Thank you for your help
Hi Amo_18,
DNA is known to show base pair opening in the Charm36 force field. This was shown by Pan et al. (NAR, 2003) and by Galindo-Murillo et al. (Biochim. Biophys. Acta, Gen.Subj. 2015). One way to fix this is by constraining the first and last basepairs. I have some posts on this here (https://gromacs.bioexcel.eu/t/constraining-terminal-basepairs-in-dna/2549/9). You could also look at Sun et al., Journal of Physical Chemistry B, 2017, which is where I got the idea from.
Hope that helps! Good luck!
Hello, please I would like you to help me with the protocol for using the charmm-gui to position the dna-protein complex. Thank you.